SMTL ID : 6u0o.1

Crystal structure of a peptidoglycan release complex, SagB-SpdC, in lipidic cubic phase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-1-1-mer

Ligands

1 x FLC: CITRATE ANION(Non-covalent)

FLC.1: 11 residues within 4Å: Chain A: F.198, L.239, I.240, F.243, E.246, I.247, G.248, D.249, I.253, I.256 Ligands: PG4.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.247 Hydrogen bonds: A:G.248, A:D.249

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.2: 7 residues within 4Å: Chain A: N.191, N.202, T.236, L.239, I.247, I.253 Ligands: FLC.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.236

1 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.3: 6 residues within 4Å: Chain A: F.31, Q.32, M.35, V.82, F.83, K.84 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:M.35, A:F.83 Hydrogen bonds: A:Q.32

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 2 residues within 4Å: Chain A: S.29, Q.32 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.29, A:Q.32, A:Q.32 SO4.5: 3 residues within 4Å: Chain B: H.38, V.39, K.40 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.40 Salt bridges: B:K.268 SO4.6: 5 residues within 4Å: Chain B: D.123, R.124, P.125, T.126, S.161 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.126, B:T.126, B:S.161 Salt bridges: B:R.124

2 x AE3: 2-(2-ETHOXYETHOXY)ETHANOL(Non-covalent)

AE3.7: 3 residues within 4Å: Chain B: I.43, I.94, Y.272 No protein-ligand interaction detected (PLIP) AE3.8: 7 residues within 4Å: Chain B: Y.147, H.151, F.218, M.230, Y.242, W.248, N.252 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.218 Hydrogen bonds: B:Y.147, B:H.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schaefer, K. et al., Structure and reconstitution of a hydrolase complex that may release peptidoglycan from the membrane after polymerization. Nat Microbiol (2021)

Release Date

2020-09-23

Peptides

Lysostaphin resistance protein A: A
LYZ2 domain-containing protein: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Lysostaphin resistance protein A

LYZ2 domain-containing protein